Revision: 18588
http://sourceforge.net/p/jmol/code/18588
Author: hansonr
Date: 2013-08-17 17:13:40 +0000 (Sat, 17 Aug 2013)
Log Message:
-----------
___JmolVersion="13.3.4_dev_2013.08.17"
new feature: show ROTATION VOLUME
-- calculates approximate best box (from 1495 quaternion-based alternatives)
-- reports "{quaternion} volume {dx dy dz}" where dx > dy > dz
new feature: show ROTATION BEST
-- just reports "{quaternion}"
new feature: quaternion("best")
-- delivers actual quaternion
new feature: rotate BEST
new feature: rotate SELECTED BEST
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/popup/MainPopupResourceBundle.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/scriptext/ScriptExt.java
trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
trunk/Jmol/src/org/jmol/util/BoxInfo.java
trunk/Jmol/src/org/jmol/util/Measure.java
trunk/Jmol/src/org/jmol/util/Quaternion.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/StateCreator.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-08-17
08:11:11 UTC (rev 18587)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-08-17
17:13:40 UTC (rev 18588)
@@ -317,7 +317,7 @@
}
public Point3fi[] getBboxVertices() {
- return boxInfo.getBboxVertices();
+ return boxInfo.getBoundBoxVertices();
}
public Map<String, Object> getBoundBoxInfo() {
@@ -3497,5 +3497,103 @@
//System.out.println(a.x + " " + a.y + " " + a.z + " ms is " + ms + " "
+ ms.enabled + " " + ms.t);
}
}
+
+ private Quaternion[] vOrientations;
+
+ public String getBoundBoxOrientation(int type, BS bsAtoms) {
+ int j0 = bsAtoms.nextSetBit(0);
+ if (j0 < 0)
+ return "{0 0 0 1}";
+ int n = (vOrientations == null ? 0 : vOrientations.length);
+ if (n == 0) {
+ V3[] av = new V3[15*15*15];
+ n = 0;
+ P4 p4 = new P4();
+ for (int i = -7; i <= 7; i++)
+ for (int j = -7; j <= 7; j++)
+ for (int k = 0; k <= 14; k++, n++)
+ if ((av[n] = V3.new3(i / 7f, j / 7f, k / 14f)).length() > 1)
+ --n;
+ vOrientations = new Quaternion[n];
+ for (int i = n; --i >= 0;) {
+ float cos = (float) Math.sqrt(1 - av[i].lengthSquared());
+ if (Float.isNaN(cos))
+ cos = 0;
+ p4.set(av[i].x, av[i].y, av[i].z, cos);
+ vOrientations[i] = Quaternion.newP4(p4);
+ }
+ }
+ P3 pt = new P3();
+ float vMin = Float.MAX_VALUE;
+ Quaternion q, qBest = null;
+ BoxInfo bBest = null;
+ float v;
+ for (int i = 0; i < n; i++) {
+ q = vOrientations[i];
+ BoxInfo b = new BoxInfo();
+ b.setMargin(0);
+ for (int j = j0; j >= 0; j = bsAtoms.nextSetBit(j + 1))
+ b.addBoundBoxPoint((P3) q.transformP2(atoms[j],
+ pt));
+ switch (type) {
+ default:
+ case T.volume:
+ case T.best:
+ v = (b.bbCorner1.x - b.bbCorner0.x) * (b.bbCorner1.y - b.bbCorner0.y)
+ * (b.bbCorner1.z - b.bbCorner0.z);
+ break;
+ case T.x:
+ v = b.bbCorner1.x - b.bbCorner0.x;
+ break;
+ case T.y:
+ v = b.bbCorner1.y - b.bbCorner0.y;
+ break;
+ case T.z:
+ v = b.bbCorner1.z - b.bbCorner0.z;
+ break;
+ }
+ if (v < vMin) {
+ qBest = q;
+ bBest = b;
+ vMin = v;
+ }
+ }
+ if (type != T.volume && type != T.best)
+ return qBest.toString();
+ // we want dz < dy < dx
+ q = Quaternion.newQ(qBest);
+ float dx = bBest.bbCorner1.x - bBest.bbCorner0.x;
+ float dy = bBest.bbCorner1.y - bBest.bbCorner0.y;
+ float dz = bBest.bbCorner1.z - bBest.bbCorner0.z;
+ if (dx < dy) {
+ pt.set(0, 0, 1);
+ q = Quaternion.newVA(pt, 90).mulQ(q);
+ float f = dx;
+ dx = dy;
+ dy = f;
+ }
+ if (dy < dz) {
+ if (dz > dx) {
+ // is dy < dx < dz
+ pt.set(0, 1, 0);
+ q = Quaternion.newVA(pt, 90).mulQ(q);
+ float f = dx;
+ dx = dz;
+ dz = f;
+ }
+ // is dy < dz < dx
+ pt.set(1, 0, 0);
+ q = Quaternion.newVA(pt, 90).mulQ(q);
+ float f = dy;
+ dy = dz;
+ dz = f;
+ }
+ v = q.getTheta();
+ if (v == 180 || v == 0)
+ return "{0 0 0 1}";
+ V3 vec = V3.new3(dx, dy, dz);
+ return q.toString() + (type == T.best ? "" : " " + vMin + " " +
Escape.eP(vec));
+ }
}
+
\ No newline at end of file
Modified: trunk/Jmol/src/org/jmol/popup/MainPopupResourceBundle.java
===================================================================
--- trunk/Jmol/src/org/jmol/popup/MainPopupResourceBundle.java 2013-08-17
08:11:11 UTC (rev 18587)
+++ trunk/Jmol/src/org/jmol/popup/MainPopupResourceBundle.java 2013-08-17
17:13:40 UTC (rev 18588)
@@ -90,7 +90,7 @@
+ "Ligand exceptWater nonWaterSolvent" },
{ "viewMenu",
- "front left right top bottom back" },
+ "best front left right top bottom back" },
{ "renderMenu",
"perspectiveDepthCB showBoundBoxCB showUNITCELLCB showAxesCB
stereoMenu - renderSchemeMenu - atomMenu labelMenu bondMenu hbondMenu
ssbondMenu - "
@@ -305,6 +305,7 @@
// not implemented { "Lipid", "SELECT lipid" },
{ "PDBnoneOfTheAbove", "SELECT not(hetero,protein,nucleic,carbohydrate)"
},
+ { "best", "rotate best -1.0" },
{ "front", Box( "moveto 2.0 front;delay 1" ) },
{ "left", Box( "moveto 1.0 front;moveto 2.0 left;delay 1" ) },
{ "right", Box( "moveto 1.0 front;moveto 2.0 right;delay 1" ) },
@@ -592,6 +593,7 @@
"invertSelection", GT._("Invert Selection"),
"viewMenu", GT._("View"),
+ "best", GT._("Best"),
"front", GT._("Front"),
"left", GT._("Left"),
"right", GT._("Right"),
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-08-17 08:11:11 UTC
(rev 18587)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-08-17 17:13:40 UTC
(rev 18588)
@@ -6559,7 +6559,7 @@
q = (chk ? new Quaternion() : viewer.getAtomQuaternion(bsCenter
.nextSetBit(0)));
} else {
- q = getQuaternionParameter(i);
+ q = getQuaternionParameter(i, null);
}
i = iToken + 1;
if (q == null)
@@ -10097,12 +10097,15 @@
case T.point4f:
case T.quaternion:
+ case T.best:
if (tok == T.quaternion)
i++;
haveRotation = true;
- q = getQuaternionParameter(i);
- rotAxis.setT(q.getNormal());
- endDegrees = q.getTheta();
+ q = getQuaternionParameter(i, isSelected || tok != T.best ? null :
viewer.getRotationQuaternion().mul(-1));
+ if (q != null) {
+ rotAxis.setT(q.getNormal());
+ endDegrees = q.getTheta();
+ }
break;
case T.axisangle:
haveRotation = true;
@@ -10333,15 +10336,26 @@
}
}
- private Quaternion getQuaternionParameter(int i) throws ScriptException {
- if (tokAt(i) == T.varray) {
+ private Quaternion getQuaternionParameter(int i, Quaternion q0)
+ throws ScriptException {
+ Quaternion q;
+ switch (tokAt(i)) {
+ case T.varray:
JmolList<SV> sv = ((SV) getToken(i)).getList();
P4 p4 = null;
if (sv.size() == 0 || (p4 = SV.pt4Value(sv.get(0))) == null)
invArg();
- return Quaternion.newP4(p4);
+ q = Quaternion.newP4(p4);
+ break;
+ case T.best:
+ if (chk)
+ return null;
+ q = Quaternion.newP4((P4) Escape.uP(viewer.getOrientationText(T.best,
null)));
+ break;
+ default:
+ q = Quaternion.newP4(getPoint4f(i));
}
- return Quaternion.newP4(getPoint4f(i));
+ return (q0 == null ? q : q.mulQ(q0));
}
JmolList<P3> getPointVector(T t, int i) throws ScriptException {
@@ -11821,12 +11835,9 @@
// deprecated
//$FALL-THROUGH$
case T.surfacedistance:
- /*
- * preferred:
- *
- * calculate surfaceDistance FROM {...} calculate surfaceDistance
WITHIN
- * {...}
- */
+ // preferred
+ // calculate surfaceDistance FROM {...}
+ // calculate surfaceDistance WITHIN {...}
boolean isFrom = false;
switch (tokAt(2)) {
case T.within:
@@ -15004,8 +15015,14 @@
if (!chk)
msg = viewer.getMeasurementInfoAsString();
break;
+ case T.rotation:
+ tok = tokAt(2);
+ if (tok == T.nada)
+ tok = T.rotation;
+ else
+ len = 3;
+ //$FALL-THROUGH$
case T.translation:
- case T.rotation:
case T.moveto:
if (!chk)
msg = viewer.getOrientationText(tok, null);
@@ -15024,7 +15041,7 @@
break;
default:
name = optParameterAsString(2);
- msg = viewer.getOrientationText(0, name);
+ msg = viewer.getOrientationText(T.name, name);
}
len = slen;
break;
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-08-17
08:11:11 UTC (rev 18587)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-08-17
17:13:40 UTC (rev 18588)
@@ -2148,6 +2148,7 @@
// quaternion(vector, theta)
// quaternion(q0, q1, q2, q3)
// quaternion("{x, y, z, w"})
+ // quaternion("best")
// quaternion(center, X, XY)
// quaternion(mcol1, mcol2)
// quaternion(q, "id", center) // draw code
@@ -2224,7 +2225,8 @@
} else if (args[0].tok == T.point4f) {
p4 = (P4) args[0].value;
} else {
- Object v = Escape.uP(SV.sValue(args[0]));
+ String s = SV.sValue(args[0]);
+ Object v = Escape.uP(s.equalsIgnoreCase("best") ?
viewer.getOrientationText(T.best, null) : s);
if (!(v instanceof P4))
return false;
p4 = (P4) v;
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2013-08-17 08:11:11 UTC (rev
18587)
+++ trunk/Jmol/src/org/jmol/script/T.java 2013-08-17 17:13:40 UTC (rev
18588)
@@ -1092,7 +1092,8 @@
public final static int back = misc | 35;
public final static int balls = misc | 36;
public final static int barb = misc | 37;
- public final static int backlit = misc | 38;
+ public final static int backlit = misc | 38;
+ public final static int best = misc | 39;
public final static int basepair = misc | 40;
public final static int binary = misc | 42;
public final static int blockdata = misc | 44;
@@ -1791,6 +1792,7 @@
"backlit", T.t(backlit),
"balls", T.t(balls),
"baseModel", T.t(basemodel), // Jmol 12.3.19
+ "best", T.t(best), // rotate BEST
"bin", T.t(bin),
"bondCount", T.t(bondcount),
"bottom", T.t(bottom),
Modified: trunk/Jmol/src/org/jmol/scriptext/ScriptExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/ScriptExt.java 2013-08-17 08:11:11 UTC
(rev 18587)
+++ trunk/Jmol/src/org/jmol/scriptext/ScriptExt.java 2013-08-17 17:13:40 UTC
(rev 18588)
@@ -3833,8 +3833,8 @@
v.addLast(ptc);
} else {
BoxInfo bbox = viewer.getBoxInfo(bs, -Math.abs(distance));
- pts[0] = bbox.getBboxVertices()[0];
- pts[1] = bbox.getBboxVertices()[7];
+ pts[0] = bbox.getBoundBoxVertices()[0];
+ pts[1] = bbox.getBoundBoxVertices()[7];
if (bs.cardinality() == 1)
v.addLast(viewer.getAtomPoint3f(bs.nextSetBit(0)));
}
Modified: trunk/Jmol/src/org/jmol/symmetry/PointGroup.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2013-08-17 08:11:11 UTC
(rev 18587)
+++ trunk/Jmol/src/org/jmol/symmetry/PointGroup.java 2013-08-17 17:13:40 UTC
(rev 18588)
@@ -411,8 +411,7 @@
if (q != null) {
pt.setT(a1);
pt.sub(center);
- q.transformP2(pt, pt);
- pt.add(center);
+ q.transformP2(pt, pt).add(center);
} else {
pt.setT(a1);
}
Modified: trunk/Jmol/src/org/jmol/util/BoxInfo.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/BoxInfo.java 2013-08-17 08:11:11 UTC (rev
18587)
+++ trunk/Jmol/src/org/jmol/util/BoxInfo.java 2013-08-17 17:13:40 UTC (rev
18588)
@@ -36,12 +36,13 @@
public class BoxInfo {
- private final P3 bbCorner0 = new P3();
- private final P3 bbCorner1 = new P3();
+ public final P3 bbCorner0 = new P3();
+ public final P3 bbCorner1 = new P3();
private final P3 bbCenter = new P3();
private final V3 bbVector = new V3();
private final Point3fi[] bbVertices = new Point3fi[8];
private boolean isScaleSet;
+ private float margin;
{
for (int i = 8; --i >= 0;)
@@ -234,7 +235,7 @@
bbCorner1 } : new P3[] { bbCorner0, bbCorner1 });
}
- public Point3fi[] getBboxVertices() {
+ public Point3fi[] getBoundBoxVertices() {
if (!isScaleSet)
setBbcage(1);
return bbVertices;
@@ -278,9 +279,13 @@
bbCorner1.set(-Float.MAX_VALUE, -Float.MAX_VALUE, -Float.MAX_VALUE);
}
+ public void setMargin(float m) {
+ margin = m;
+ }
+
public void addBoundBoxPoint(P3 pt) {
isScaleSet = false;
- addPoint(pt, bbCorner0, bbCorner1, 0);
+ addPoint(pt, bbCorner0, bbCorner1, margin);
}
public static void addPoint(P3 pt, P3 xyzMin, P3 xyzMax, float margin) {
@@ -345,6 +350,4 @@
&& pt.z >= bbCorner0.z && pt.z <= bbCorner1.z);
}
-
-
}
Modified: trunk/Jmol/src/org/jmol/util/Measure.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Measure.java 2013-08-17 08:11:11 UTC (rev
18587)
+++ trunk/Jmol/src/org/jmol/util/Measure.java 2013-08-17 17:13:40 UTC (rev
18588)
@@ -577,8 +577,7 @@
for (int i = n + 1; --i >= 1;) {
ptAnew.setT(ptsA[i]);
ptAnew.sub(cA);
- q.transformP2(ptAnew, ptAnew);
- ptAnew.add(cB);
+ q.transformP2(ptAnew, ptAnew).add(cB);
sum2 += ptAnew.distanceSquared(ptsB[i]);
}
return (float) Math.sqrt(sum2 / n);
Modified: trunk/Jmol/src/org/jmol/util/Quaternion.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Quaternion.java 2013-08-17 08:11:11 UTC
(rev 18587)
+++ trunk/Jmol/src/org/jmol/util/Quaternion.java 2013-08-17 17:13:40 UTC
(rev 18588)
@@ -600,10 +600,11 @@
return ptNew;
}
- public void transformP2(Tuple3f pt, Tuple3f ptNew) {
+ public Tuple3f transformP2(Tuple3f pt, Tuple3f ptNew) {
if (mat == null)
setMatrix();
mat.transform2(pt, ptNew);
+ return ptNew;
}
public V3 transform(V3 v) {
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-17 08:11:11 UTC
(rev 18587)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-17 17:13:40 UTC
(rev 18588)
@@ -11,10 +11,22 @@
# The quotes above look odd for a parameter file, but they are
# important for the JavaScript version of Jmol.
-___JmolVersion="13.3.4_dev_2013.08.16"
+___JmolVersion="13.3.4_dev_2013.08.17"
+new feature: show ROTATION VOLUME
+ -- calculates approximate best box (from 1495 quaternion-based alternatives)
+ -- reports "{quaternion} volume {dx dy dz}" where dx > dy > dz
+new feature: show ROTATION BEST
+ -- just reports "{quaternion}"
+new feature: quaternion("best")
+ -- delivers actual quaternion
+new feature: rotate BEST
+new feature: rotate SELECTED BEST
+
bug fix: CIF reader does not find Hall name for space groups
-NEW FEATURE: set platformSpeed [0 to 10] (includes wireframeRotation along
with cartoons and surfaces)
+
+new feature: set platformSpeed [0 to 10] (includes wireframeRotation along
with cartoons and surfaces)
+
bug fix: binding names not included in SHOW MOUSE
bug fix: "single" touch can fire double-click
bug fix: {x}.tensor() command fails when no atom tensors
Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2013-08-17 08:11:11 UTC
(rev 18587)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2013-08-17 17:13:40 UTC
(rev 18588)
@@ -769,7 +769,7 @@
appendCmd(commands, "set navigationMode true");
appendCmd(commands, viewer.getBoundBoxCommand(false));
appendCmd(commands, "center " + Escape.eP(tm.fixedRotationCenter));
- commands.append(viewer.getOrientationText(T.state, null));
+ commands.append(viewer.getOrientationText(T.name, null));
appendCmd(commands, moveToText);
if (tm.stereoMode != EnumStereoMode.NONE)
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-08-17 08:11:11 UTC (rev
18587)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-08-17 17:13:40 UTC (rev
18588)
@@ -1436,9 +1436,20 @@
}
public String getOrientationText(int type, String name) {
- return (name == null && type != T.state ?
transformManager.getOrientationText(type)
- : stateManager.getSavedOrientationText(name));
- }
+ switch (type) {
+ case T.volume:
+ case T.best:
+ case T.x:
+ case T.y:
+ case T.z:
+ case T.quaternion:
+ return modelSet.getBoundBoxOrientation(type, getSelectionSet(false));
+ case T.name:
+ return stateManager.getSavedOrientationText(name);
+ default:
+ return transformManager.getOrientationText(type);
+ }
+ }
Map<String, Object> getOrientationInfo() {
return transformManager.getOrientationInfo();
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